[gentoo-commits] proj/sci:master commit in: sci-chemistry/coot/files/, sci-chemistry/coot/
commit: ac002458a28fad508b966a6e7ce571603fb6b603
Author: Aisha Tammy aisha cc>
AuthorDate: Tue Sep 22 13:35:27 2020 +
Commit: Aisha Tammy aisha cc>
CommitDate: Tue Sep 22 13:35:27 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=ac002458
sci-chemistry/coot: drop package
maintainer AWOL
Package-Manager: Portage-3.0.7, Repoman-3.0.1
Signed-off-by: Aisha Tammy aisha.cc>
sci-chemistry/coot/coot-.ebuild| 177 -
sci-chemistry/coot/files/coot--desktop.patch | 21 ---
sci-chemistry/coot/files/coot--libguile.patch | 29
sci-chemistry/coot/files/coot--libtool.patch | 39 -
.../coot/files/coot--sandbox-icons.patch | 16 --
sci-chemistry/coot/metadata.xml| 12 --
6 files changed, 294 deletions(-)
diff --git a/sci-chemistry/coot/coot-.ebuild
b/sci-chemistry/coot/coot-.ebuild
deleted file mode 100644
index f13e9b681..0
--- a/sci-chemistry/coot/coot-.ebuild
+++ /dev/null
@@ -1,177 +0,0 @@
-# Copyright 1999-2018 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit autotools git-r3 python-single-r1 toolchain-funcs versionator
-
-MY_S2_PV=$(replace_version_separator 2 - ${PV})
-MY_S2_P=${PN}-${MY_S2_PV/pre1/pre-1}
-MY_S_P=${MY_S2_P}-${PR/r/revision-}
-MY_PV=${PV}
-MY_P=${PN}-${MY_PV}
-
-DESCRIPTION="Crystallographic Object-Oriented Toolkit"
-HOMEPAGE="https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/;
-SRC_URI="test? (
https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/data/greg-data.tar.gz )"
-EGIT_REPO_URI="https://github.com/pemsley/coot.git;
-
-SLOT="0"
-LICENSE="GPL-3"
-KEYWORDS=""
-IUSE="+openmp static-libs test"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-AUTOTOOLS_IN_SOURCE_BUILD=1
-
-SCIDEPS="
- sci-libs/libccp4
- sci-libs/clipper
- >=sci-libs/coot-data-2
- >=sci-libs/gsl-1.3
- sci-libs/fftw:2.1=
- sci-libs/mmdb:2
- sci-libs/monomer-db
- sci-libs/ssm
- sci-chemistry/reduce
- sci-chemistry/probe"
-
-XDEPS="
- gnome-base/libgnomecanvas
- gnome-base/librsvg:2
- media-libs/libpng:0=
- media-libs/freeglut
- x11-libs/gtk+:2
- x11-libs/goocanvas:0
- x11-libs/gtkglext
- virtual/opengl"
-
-SCHEMEDEPS="
- dev-scheme/net-http
- dev-scheme/guile-gui
- >=dev-scheme/guile-lib-0.1.6
- dev-scheme/guile-www
- >=x11-libs/guile-gtk-2.1"
-
-RDEPEND="
- ${SCIDEPS}
- ${XDEPS}
- ${SCHEMEDEPS}
- ${PYTHON_DEPS}
- dev-db/sqlite:3
- dev-libs/boost:0=[python,${PYTHON_USEDEP}]
- dev-libs/glib:2
- >=dev-libs/gmp-4.2.2-r2:0=
- dev-python/pygobject:2[${PYTHON_USEDEP}]
- dev-python/pygtk:2[${PYTHON_USEDEP}]
- >=net-misc/curl-7.19.6
- net-dns/libidn:0
- sys-libs/readline:0=
- "
-DEPEND="${RDEPEND}
- virtual/pkgconfig
- >=sys-devel/libtool-2.4-r2
- dev-lang/swig
- sys-devel/bc
- test? ( dev-scheme/greg )"
-
-pkg_setup() {
- if use openmp; then
- tc-has-openmp || die "Please use an OPENMP capable compiler"
- fi
- python-single-r1_pkg_setup
-}
-
-PATCHES=(
- "${FILESDIR}"/${P}-desktop.patch
- "${FILESDIR}"/${P}-sandbox-icons.patch
- "${FILESDIR}"/${P}-libtool.patch
- "${FILESDIR}"/${P}-libguile.patch
-)
-
-src_unpack() {
- git-r3_src_unpack
- if use test; then
- cd "${S}" || die
- unpack ${A}
- ln -sf . "${S}"/coot-ccp4 || die
- fi
-}
-
-src_prepare() {
- sed \
- -e '/export LD_LIBRARY/s:^:#:g' \
- -i src/coot.in || die
-
- sed \
- -e
"s:AM_COOT_SYS_BUILD_TYPE:COOT_SYS_BUILD_TYPE=Gentoo-Linux-${EPYTHON}-gtk2 ;
AC_MSG_RESULT([\$COOT_SYS_BUILD_TYPE]); AC_SUBST(COOT_SYS_BUILD_TYPE):g" \
- -i configure.ac || die
-
- default
- eautoreconf
-}
-
-src_configure() {
- # All the --with's are used to activate various parts.
- # Yes, this is broken behavior.
- local myeconfargs=(
- --with-goocanvas-prefix="${EPREFIX}/usr"
- --with-guile="${EPREFIX}/usr"
- --with-python="${EPREFIX}/usr"
- --with-guile-gtk
- --with-pygtk="${EPREFIX}/usr"
- --with-sqlite3
- --with-boost="${EPREFIX}/usr"
- )
- econf ${myeconfargs[@]}
-}
-
-src_test() {
- source "${EPREFIX}/etc/profile.d/40ccp4.setup.sh"
- mkdir "${T}"/coot_test || die
-
- export COOT_STANDARD_RESIDUES="${S}/standard-residues.pdb"
- export COOT_SCHEME_DIR="${S}/scheme/"
- export COOT_RESOURCES_FILE="${S}/cootrc"
- export COOT_PIXMAPS_DIR="${S}/pixmaps/"
- export COOT_DATA_DIR="${S}/"
- export COOT_PYTHON_DIR="${S}/python/"
- export
[gentoo-commits] proj/sci:master commit in: sci-chemistry/coot/files/, sci-chemistry/coot/
commit: 20873c20812ebb870e9fdce159daa1da97cea074
Author: Justin Lecher gentoo org>
AuthorDate: Tue Sep 15 13:34:07 2015 +
Commit: Justin Lecher gentoo org>
CommitDate: Tue Sep 15 13:34:07 2015 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=20873c20
sci-chemistry/coot: Fix for latest HEAD
Package-Manager: portage-2.2.20.1
Signed-off-by: Justin Lecher gentoo.org>
sci-chemistry/coot/coot-.ebuild | 76 +-
sci-chemistry/coot/files/-pc.patch| 1047 -
sci-chemistry/coot/files/coot--desktop.patch | 21 +
sci-chemistry/coot/files/coot--libguile.patch | 29 +
sci-chemistry/coot/files/coot--libtool.patch | 39 +
5 files changed, 126 insertions(+), 1086 deletions(-)
diff --git a/sci-chemistry/coot/coot-.ebuild
b/sci-chemistry/coot/coot-.ebuild
index 1ea16a3..d6b0be9 100644
--- a/sci-chemistry/coot/coot-.ebuild
+++ b/sci-chemistry/coot/coot-.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -8,7 +8,7 @@ PYTHON_COMPAT=( python2_7 )
AUTOTOOLS_AUTORECONF="true"
-inherit autotools-utils python-single-r1 subversion toolchain-funcs versionator
+inherit autotools-utils git-r3 python-single-r1 toolchain-funcs versionator
MY_S2_PV=$(replace_version_separator 2 - ${PV})
MY_S2_P=${PN}-${MY_S2_PV/pre1/pre-1}
@@ -17,9 +17,9 @@ MY_PV=${PV}
MY_P=${PN}-${MY_PV}
DESCRIPTION="Crystallographic Object-Oriented Toolkit for model building,
completion and validation"
-HOMEPAGE="http://www.biop.ox.ac.uk/coot/;
-SRC_URI="test? (
http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/data/greg-data.tar.gz )"
-ESVN_REPO_URI="http://coot.googlecode.com/svn/trunk;
+HOMEPAGE="https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/;
+SRC_URI="test? (
https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/data/greg-data.tar.gz )"
+EGIT_REPO_URI="https://github.com/pemsley/coot.git;
SLOT="0"
LICENSE="GPL-3"
@@ -31,25 +31,26 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}"
AUTOTOOLS_IN_SOURCE_BUILD=1
SCIDEPS="
- >=sci-libs/ccp4-libs-6.1
+ sci-libs/libccp4
sci-libs/clipper
>=sci-libs/coot-data-2
>=sci-libs/gsl-1.3
- >=sci-libs/mmdb-1.23
- sci-libs/ssm
+ sci-libs/fftw:2.1=
+ sci-libs/mmdb:2
sci-libs/monomer-db
+ sci-libs/ssm
sci-chemistry/reduce
- sci-chemistry/refmac
sci-chemistry/probe"
XDEPS="
gnome-base/libgnomecanvas
gnome-base/librsvg:2
- media-libs/libpng
+ media-libs/libpng:0=
media-libs/freeglut
x11-libs/gtk+:2
x11-libs/goocanvas:0
- x11-libs/gtkglext"
+ x11-libs/gtkglext
+ virtual/opengl"
SCHEMEDEPS="
dev-scheme/net-http
@@ -63,18 +64,23 @@ RDEPEND="
${XDEPS}
${SCHEMEDEPS}
${PYTHON_DEPS}
+ dev-db/sqlite:3
+ dev-libs/boost:0=[python,${PYTHON_USEDEP}]
+ dev-libs/glib:2
+ >=dev-libs/gmp-4.2.2-r2:0=
+ dev-python/pygobject:2[${PYTHON_USEDEP}]
dev-python/pygtk:2[${PYTHON_USEDEP}]
- >=dev-libs/gmp-4.2.2-r2
>=net-misc/curl-7.19.6
- net-dns/libidn"
+ net-dns/libidn
+ sys-libs/readline:0=
+ "
DEPEND="${RDEPEND}
+ virtual/pkgconfig
>=sys-devel/libtool-2.4-r2
dev-lang/swig
sys-devel/bc
test? ( dev-scheme/greg )"
-S="${WORKDIR}"
-
pkg_setup() {
if use openmp; then
tc-has-openmp || die "Please use an OPENMP capable compiler"
@@ -83,53 +89,44 @@ pkg_setup() {
}
PATCHES=(
- "${FILESDIR}"/${PV}-pc.patch
+ "${FILESDIR}"/${P}-desktop.patch
"${FILESDIR}"/${P}-sandbox-icons.patch
+ "${FILESDIR}"/${P}-libtool.patch
+ "${FILESDIR}"/${P}-libguile.patch
)
src_unpack() {
- subversion_src_unpack
+ git-r3_src_unpack
if use test; then
+ cd "${S}" || die
unpack ${A}
- ln -sf . "${S}"/coot-ccp4
+ ln -sf . "${S}"/coot-ccp4 || die
fi
}
src_prepare() {
sed \
-e
"s:AM_COOT_SYS_BUILD_TYPE:COOT_SYS_BUILD_TYPE=Gentoo-Linux-${EPYTHON}-gtk2 ;
AC_MSG_RESULT([\$COOT_SYS_BUILD_TYPE]); AC_SUBST(COOT_SYS_BUILD_TYPE):g" \
- -i configure.in || die
+ -i configure.ac || die
autotools-utils_src_prepare
-
- cat >> src/svn-revision.cc <<- EOF
- extern "C" {
- int svn_revision() {
- return ${ESVN_WC_REVISION:-0};
- }
- }
- EOF
}
src_configure() {
# All the --with's are used to activate various parts.
# Yes, this is broken behavior.
local myeconfargs=(
- --includedir='${prefix}/include/coot'
--with-goocanvas-prefix="${EPREFIX}/usr"
- --with-guile
+
[gentoo-commits] proj/sci:master commit in: sci-chemistry/coot/files/, sci-chemistry/coot/
commit: 6a07207adec9b6152a0ab28c72f724c3972f1e8e
Author: Justin Lecher jlec AT gentoo DOT org
AuthorDate: Mon Jun 30 19:02:25 2014 +
Commit: Justin Lecher jlec AT gentoo DOT org
CommitDate: Mon Jun 30 19:02:25 2014 +
URL:
http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=6a07207a
sci-chemistry/coot: Fix sandbox violation
Package-Manager: portage-2.2.10
---
sci-chemistry/coot/ChangeLog | 8
sci-chemistry/coot/coot-.ebuild| 5 -
sci-chemistry/coot/files/coot--sandbox-icons.patch | 16
3 files changed, 28 insertions(+), 1 deletion(-)
diff --git a/sci-chemistry/coot/ChangeLog b/sci-chemistry/coot/ChangeLog
index cee77b1..cd498bb 100644
--- a/sci-chemistry/coot/ChangeLog
+++ b/sci-chemistry/coot/ChangeLog
@@ -2,6 +2,14 @@
# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 30 Jun 2014; Justin Lecher j...@gentoo.org coot-.ebuild,
+ +files/coot--sandbox-icons.patch:
+ Fix sandbox violation
+
+ 30 Jun 2014; Justin Lecher j...@gentoo.org coot-.ebuild,
+ +files/coot--sandbox-icons.patch:
+ Fix sandbox violation
+
08 Jun 2014; Justin Lecher j...@gentoo.org coot-.ebuild:
Fix problem with shebang correction
diff --git a/sci-chemistry/coot/coot-.ebuild
b/sci-chemistry/coot/coot-.ebuild
index f0fd7dc..79aed91 100644
--- a/sci-chemistry/coot/coot-.ebuild
+++ b/sci-chemistry/coot/coot-.ebuild
@@ -82,7 +82,10 @@ pkg_setup() {
python-single-r1_pkg_setup
}
-PATCHES=( ${FILESDIR}/${PV}-pc.patch )
+PATCHES=(
+ ${FILESDIR}/${PV}-pc.patch
+ ${FILESDIR}/${P}-sandbox-icons.patch
+)
src_unpack() {
subversion_src_unpack
diff --git a/sci-chemistry/coot/files/coot--sandbox-icons.patch
b/sci-chemistry/coot/files/coot--sandbox-icons.patch
new file mode 100644
index 000..2a9ff2d
--- /dev/null
+++ b/sci-chemistry/coot/files/coot--sandbox-icons.patch
@@ -0,0 +1,16 @@
+ pixmaps/icons/Makefile.am | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/pixmaps/icons/Makefile.am b/pixmaps/icons/Makefile.am
+index 0c183ae..dddc11a 100644
+--- a/pixmaps/icons/Makefile.am
b/pixmaps/icons/Makefile.am
+@@ -11,6 +11,6 @@ install-data-local:
+ CONTEXT=` echo $$icon | cut -d_ -f2`; \
+ SIZE=`echo $$icon | cut -d_ -f3`; \
+ ICONFILE=`echo $$icon | cut -d_ -f4`; \
+- mkdir -p $(datadir)/icons/$$THEME/$$SIZE/$$CONTEXT; \
+- $(INSTALL_DATA) $(srcdir)/$$icon
$(datadir)/icons/$$THEME/$$SIZE/$$CONTEXT/$$ICONFILE; \
++ mkdir -p $(DESTDIR)$(datadir)/icons/$$THEME/$$SIZE/$$CONTEXT; \
++ $(INSTALL_DATA) $(srcdir)/$$icon
$(DESTDIR)$(datadir)/icons/$$THEME/$$SIZE/$$CONTEXT/$$ICONFILE; \
+ done;
